X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O08PDB entry 3O08

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.62921microL reservoir + 1microL protein, reservoir: 2.4M di-ammonia phosphate, 0.1M Ches pH 9.6, protein: 10mg/ml Klhxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 1mM xylose, 1mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.4649.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.54α = 90
b = 93.59β = 102.42
c = 114.29γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD1st mirror: Silicon, active surface 50 nm Rh-coated; 2nd mirror: Glas, active surface 50 nm Rh-coated2009-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.483099.60.03121.73.6172567171952-326.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.481.5299.80.4912.5312664

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3O081.4829.12170225172399.680.16730.167120.18391RANDOM23.742
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.42-0.671.08-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.274
r_dihedral_angle_4_deg18.247
r_dihedral_angle_3_deg11.524
r_scangle_it5.859
r_dihedral_angle_1_deg5.54
r_scbond_it3.548
r_mcangle_it2.12
r_angle_refined_deg1.409
r_mcbond_it1.272
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.274
r_dihedral_angle_4_deg18.247
r_dihedral_angle_3_deg11.524
r_scangle_it5.859
r_dihedral_angle_1_deg5.54
r_scbond_it3.548
r_mcangle_it2.12
r_angle_refined_deg1.409
r_mcbond_it1.272
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7269
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms45

Software

Software
Software NamePurpose
MAR345data collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling